Mercurial > repos > lz_hust > gatktools
changeset 1:d0a9360bb58e draft
Uploaded
| author | lz_hust |
|---|---|
| date | Fri, 31 May 2019 23:08:21 -0400 |
| parents | 551fc755f196 |
| children | e109a0e6ffc9 |
| files | fasta-tool.pl |
| diffstat | 1 files changed, 960 insertions(+), 0 deletions(-) [+] |
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0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> + Jump to 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data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"LOG_IN","client_id":null,"originating_request_id":"8338:3535:6E3933:C6369E:5CF1EC24","originating_url":"https://github.com/huster16/fasta-tool/blob/master/fasta-tool.pl","referrer":null,"user_id":null}}" data-hydro-click-hmac="b81e5b1da80f5bf147c6fc41df2f6260716dc7bb9d4f22ed5e3c9d679abe0d30" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in" href="/login?return_to=%2Fhuster16%2Ffasta-tool%2Fblob%2Fmaster%2Ffasta-tool.pl"> + Sign in +</a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header 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class="pl-c">#</span> usage : perl toolExample.pl <FASTA file> <output file></span></td> + </tr> + <tr> + <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> + <td id="LC4" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> + <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-c1">open</span> (IN, <span class="pl-s"><span class="pl-pds">"</span><<span class="pl-smi">$ARGV</span>[0]<span class="pl-pds">"</span></span>);</td> + </tr> + <tr> + <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> + <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-c1">open</span> (OUT, <span class="pl-s"><span class="pl-pds">"</span>><span class="pl-smi">$ARGV</span>[1]<span class="pl-pds">"</span></span>);</td> + </tr> + <tr> + <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> + <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-k">while</span> (<IN>) {</td> + </tr> + <tr> + <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> + <td id="LC8" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">chop</span>;</td> + </tr> + <tr> + <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> + <td id="LC9" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> (<span class="pl-sr"><span class="pl-pds"><span class="pl-c1">m</span>/</span>^><span class="pl-pds">/</span></span>) {</td> + </tr> + <tr> + <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> + <td id="LC10" class="blob-code blob-code-inner js-file-line"> <span class="pl-sr"><span class="pl-pds"><span class="pl-c1">s</span>/</span>^></span><span class="pl-sr"><span class="pl-pds">//</span></span>;</td> + </tr> + <tr> + <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> + <td id="LC11" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> (<span class="pl-smi">$.</span> > 1) {</td> + </tr> + <tr> + <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> + <td id="LC12" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span> OUT <span class="pl-c1">sprintf</span>(<span class="pl-s"><span class="pl-pds">"</span>%.3f<span class="pl-pds">"</span></span>, <span class="pl-smi">$gc</span>/<span class="pl-smi">$length</span>) . <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</td> + </tr> + <tr> + <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> + <td id="LC13" class="blob-code blob-code-inner js-file-line"> }</td> + </tr> + <tr> + <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> + <td id="LC14" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">$gc</span> = 0;</td> + </tr> + <tr> + <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> + <td id="LC15" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">$length</span> = 0;</td> + </tr> + <tr> + <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> + <td id="LC16" class="blob-code blob-code-inner js-file-line"> } <span class="pl-k">else</span> {</td> + </tr> + <tr> + <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> + <td id="LC17" class="blob-code blob-code-inner js-file-line"> ++<span class="pl-smi">$gc</span> <span class="pl-k">while</span> <span class="pl-sr"><span class="pl-pds"><span class="pl-c1">m</span>/</span><span class="pl-c1">[gc]</span><span class="pl-pds">/</span></span><span class="pl-sr"><span class="pl-pds"><span class="pl-k">ig</span></span></span>;</td> + </tr> + <tr> + <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> + <td id="LC18" class="blob-code blob-code-inner js-file-line"> <span class="pl-smi">$length</span> += <span class="pl-c1">length</span> <span class="pl-smi">$_</span>;</td> + </tr> + <tr> + <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> + <td id="LC19" class="blob-code blob-code-inner js-file-line"> }</td> + </tr> + <tr> + <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> + <td id="LC20" class="blob-code blob-code-inner js-file-line">}</td> + </tr> + <tr> + <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> + <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-c1">print</span> OUT <span class="pl-c1">sprintf</span>(<span class="pl-s"><span class="pl-pds">"</span>%.3f<span class="pl-pds">"</span></span>, <span class="pl-smi">$gc</span>/<span class="pl-smi">$length</span>) . <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</td> + </tr> + <tr> + <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> + <td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-c1">close</span>( IN );</td> + </tr> + <tr> + <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> + <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-c1">close</span>( OUT );</td> + </tr> +</table> + + <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true"> + <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar"> + <svg class="octicon octicon-kebab-horizontal" viewBox="0 0 13 16" version="1.1" width="13" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm5 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zM13 7.5a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z"/></svg> + </summary> + <details-menu> + <ul class="BlobToolbar-dropdown dropdown-menu 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